Singularity #67

Workflow file for this run

	name: Test Harpy Modules

	on:
	push:
	branches:
	- 'dev'
	pull_request:
	branches:
	- dev

	# Cancel in progress workflows on pull_requests.
	# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-a-fallback-value
	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	env:
	CACHE_NUMBER: 0 # increase to reset cache manually

	jobs:
	changes:
	name: detect file changes
	runs-on: ubuntu-latest
	# Required permissions
	permissions:
	pull-requests: read
	# Set job outputs to values from filter step
	outputs:
	preflight: ${{ steps.filter.outputs.preflight }}
	demux: ${{ steps.filter.outputs.demux }}
	qc: ${{ steps.filter.outputs.qc }}
	bwa: ${{ steps.filter.outputs.bwa }}
	ema: ${{ steps.filter.outputs.ema }}
	minimap: ${{ steps.filter.outputs.minimap }}
	mpileup: ${{ steps.filter.outputs.mpileup }}
	freebayes: ${{ steps.filter.outputs.freebayes }}
	leviathan: ${{ steps.filter.outputs.leviathan }}
	naibr: ${{ steps.filter.outputs.naibr }}
	impute: ${{ steps.filter.outputs.impute }}
	phase: ${{ steps.filter.outputs.phase }}
	simvars: ${{ steps.filter.outputs.simvars }}
	simreads: ${{ steps.filter.outputs.simreads }}
	steps:
	- name: checkout
	uses: actions/checkout@v4
	- name: check which files changed
	uses: dorny/paths-filter@v3
	id: filter
	with:
	base: 'dev'
	filters: .github/filters.yml

	pkgbuild:
	name: harpy installation
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh

	test_dmux_gen1:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.demux == 'true' && needs.pkgbuild.result == 'success' }}
	name: test demux gen1
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: harpy demultiplex
	run: harpy demultiplex gen1 --snakemake "--apptainer-args --sandbox" --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*
	shell: micromamba-shell {0}

	test_preflight:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.preflight == 'true' && needs.pkgbuild.result == 'success' }}
	name: test preflight
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: test preflight fastq
	shell: micromamba-shell {0}
	run: harpy preflight fastq --snakemake "--apptainer-args sandbox" test/fastq
	- name: test preflight bam
	if: always()
	shell: micromamba-shell {0}
	run: harpy preflight bam --snakemake "--apptainer-args sandbox" test/bam

	test_qc:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.qc == 'true' && needs.pkgbuild.result == 'success' }}
	name: test qc
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: harpy qc
	shell: micromamba-shell {0}
	run: harpy qc -x "--trim_poly_g" --snakemake "--show-failed-logs --apptainer-args sandbox" test/fastq
	- name: harpy qc skip adapter trimming
	if: always()
	shell: micromamba-shell {0}
	run: harpy qc -a --snakemake "--show-failed-logs --apptainer-args sandbox" test/fastq

	test_bwa:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.bwa == 'true' && needs.pkgbuild.result == 'success' }}
	name: test align BWA
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: test bwa
	shell: micromamba-shell {0}
	run: harpy align bwa -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-A 2" test/fastq

	test_ema:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.ema == 'true' && needs.pkgbuild.result == 'success' }}
	name: test align EMA
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: test ema
	shell: micromamba-shell {0}
	run: harpy align ema --ema-bins 150 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-d" test/fastq

	test_minimap:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.minimap == 'true' && needs.pkgbuild.result == 'success' }}
	name: test align minimap
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: test minimap
	shell: micromamba-shell {0}
	run: harpy align minimap -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "--seed 13" test/fastq

	test_mpileup:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.mpileup == 'true' && needs.pkgbuild.result == 'success' }}
	name: test mpileup
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: snp mpileup
	shell: micromamba-shell {0}
	run: harpy snp mpileup -r test/positions.bed -g test/genome/genome.fasta.gz -x "--ignore-RG" test/bam
	- name: snp mpileup-pop
	shell: micromamba-shell {0}
	run: harpy snp mpileup -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups -s "--apptainer-args --sandbox" test/bam

	test_freebayes:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.freebayes == 'true' && needs.pkgbuild.result == 'success' }}
	name: test freebayes
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: snp freebayes
	shell: micromamba-shell {0}
	run: harpy snp freebayes -r test/positions.bed -g test/genome/genome.fasta.gz -x "-g 200" test/bam
	- name: snp freebayes-pop
	shell: micromamba-shell {0}
	run: harpy snp freebayes -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups test/bam

	test_impute:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.impute == 'true' && needs.pkgbuild.result == 'success' }}
	name: test impute
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: impute
	shell: micromamba-shell {0}
	run: harpy impute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
	- name: impute from vcf
	shell: micromamba-shell {0}
	if: always()
	run: harpy impute --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam

	test_phase:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.phase == 'true' && needs.pkgbuild.result == 'success' }}
	name: test phase
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: phase
	shell: micromamba-shell {0}
	run: harpy phase --vcf test/vcf/test.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" -x "--max_iter 10001" test/bam
	- name: phase with indels
	shell: micromamba-shell {0}
	if: always()
	run: harpy phase --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
	- name: phase from vcf
	shell: micromamba-shell {0}
	if: always()
	run: harpy phase --vcf-samples -o phasevcf --vcf test/vcf/test.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam

	test_leviathan:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.leviathan == 'true' && needs.pkgbuild.result == 'success' }}
	name: test sv leviathan
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: leviathan
	shell: micromamba-shell {0}
	run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-M 2002" test/bam
	continue-on-error: true
	- name: leviathan-pop
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam

	test_naibr:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.naibr == 'true' && needs.pkgbuild.result == 'success' }}
	name: test sv naibr
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: naibr
	shell: micromamba-shell {0}
	run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/naibr --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-min_sv 5000" test/bam_phased && rm -r Genome
	- name: naibr pop
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam_phased && rm -r Genome
	- name: naibr with phasing
	if: always()
	shell: micromamba-shell {0}
	run: \|
	harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam && rm -r Genome
	- name: naibr pop with phasing
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam && rm -r Genome


	test_simulate_variants:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.simvars == 'true' && needs.pkgbuild.result == 'success' }}
	name: test simulate variants
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	shell: micromamba-shell {0}
	- name: simulate random snps/indels
	shell: micromamba-shell {0}
	run: \|
	harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
	harpy simulate snpindel --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/sim.snpindel.indel.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
	- name: simulate inversions
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate inversion --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate inversion --prefix Simulate/invvcf --vcf Simulate/inversion/sim.inversion.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
	- name: simulate cnv
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate cnv --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate cnv --prefix Simulate/cnvvcf --vcf Simulate/cnv/sim.cnv.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
	- name: simulate translocations
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate translocation --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate translocation --prefix Simulate/transvcf --vcf Simulate/translocation/sim.translocation.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz

	test_simulate_linkedreads:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.simreads == 'true' && needs.pkgbuild.result == 'success' }}
	name: test simulate linkedreads
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: simulate linked reads
	shell: micromamba-shell {0}
	run: harpy simulate linkedreads --snakemake "--show-failed-logs --apptainer-args sandbox" -t 4 -n 2 -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz

	test_extras:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.extras == 'true' && needs.pkgbuild.result == 'success' }}
	name: test harpy extras
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: setup mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: harpy stitchparams
	shell: micromamba-shell {0}
	run: harpy stitchparams -o params.file
	- name: harpy popgroup
	shell: micromamba-shell {0}
	run: harpy popgroup test/fastq

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Singularity #67

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Singularity #67

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